The Catholic Bishops have just issued a formal statement on the contraceptive mandate. It is well thought out and puts forward their position clearly, whether one agrees with that position or not. One can read the text on Rocco Palmo's 'Whispers in the Loggia' blog (and elsewhere, I'm sure). http://whispersintheloggia.blogspot.com/2012/03/bishops-on-religious-freedom-strongly.html
Honestly, I can see both sides here. I understand those who see it as an infringement of religious freedom. But the government is not ordering any church -- nor individual, for that matter -- to provide contraception. It is ordering them to pay (via their insurance) should their employee choose to use it (and not direct Church employees, it should be noted -- those are exempt).
I see this as more akin to a pacifist being required to pay taxes to support a war. He is exempt from actually fighting.
This whole problem would not exist had we gone with a single payer everyone-on-Medicare sort of approach. That is probably coming. In the meantime, perhaps it would be best if this whole thing ended up in the Supreme Court so we get a definitive definition. At least until a later Court changes it.